ABCC : Application's document Page

TNT

5f

XRay/NMR Structure Refinement

Dale E Tronrud and Lynn F. Ten Eyck

TNT is a program package which is used to "refine" models of
macromolecules.  It has been used for a number of years to produce
improved models based upon X-ray diffraction data and the knowledge
of chemical structures learned from small molecules. 

How to run the test cases under /usr/local/fbscapp/tnt/doc/examples
directory?

The following test assumes that the user wants to try the test case
of refining a protein-inbibitor complex of the enzyme Thermolysin.

1) cp -r /usr/local/fbscapp/tnt/doc/examples/phrm .
2) cd phrm 
3) cp /usr/local/fbscapp/tnt/data/symmetry/p6122.dat .
4) cp phrm.cor init.cor
5) edit the file  tln_phrm.tnt
    and change the following line

   INCLUDE ../../../data/symmetry/p6122.dat

    to 

    INCLUDE ./p6122.dat
    
6) To run 30 cycles of refinement, type
    tnt 1 30

You can also use the other predefined TNT commands,
like "geometry", "rfactor", "to_pdb" along with a
coordinate file. 

 For example,
  geometry phrm.cor

For more information, visit TNT's homepage at the following
link
 http://www.uoxray.uoregon.edu/tnt/welcome.html

SGI

/usr/local/fbscapp/tnt
 

please add the following line 
to your (.login)

source /usr/local/fbscapp/tnt/bin/logicals

/usr/local/fbscapp/tnt/doc/guide_5f.pdf
/usr/local/fbscapp/tnt/doc/guide_5f.ps
/usr/local/fbscapp/tnt/doc/manual_5f.ps

Dr. Karol Miaskiewicz
        (or)    
Dr. Sarangan Ravichandran

ravichas

2002-07-12

ravichas

2002-07-12